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98 results for “lipid bilayer”
Simulations DSPC bilayers (512 lipids) using charmm36 ff in gromacs
<p>Collection simulations of DSPC (512 lipids) bilayers in gromacs using the charmm36 force field. Temperatures of 333 and 338 K are included. The list of systems can be found below:</p> <p>1) DSPC_512_NaCl_150mM_333K (620ns)<br> 2) DSPC_512_NaCl_150mM_338K (500ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
Simulations DPPC bilayers (512 lipids) using charmm36 ff in gromacs
<p>Collection simulations of DPPC (512 lipids) bilayers in gromacs using the charmm36 force field. Several temperatures between 315 and 338 K are included. The list of systems can be found below where the several parameter are:</p> <p>1) DPPC_512_NaCl_150mM_315K_v-rescale (500ns)<br> 2) DPPC_512_NaCl_150mM_320K (700ns)<br> 3) DPPC_512_NaCl_150mM_320K_v-rescale (500ns)<br> 4) DPPC_512_NaCl_150mM_322K_v-rescale (700ns)<br> 5) DPPC_512_NaCl_150mM_325K (500ns)<br> 6) DPPC_512_NaCl_150mM_325K_v-rescale (500ns)<br> 7) DPPC_512_NaCl_150mM_325K_cutoff09 (500ns)<br> 8) DPPC_512_NaCl_150mM_325K_MEMB_338K (500ns)<br> 9) DPPC_512_NaCl_150mM_338K (500ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
Set simulations small pure bilayers (72 lipids) using charmm36 ff in gromacs (DPPC, POPC)
<p>Collection simulations of DPPC and POPC bilayers in gromacs using the charmm36 force field. The list of systems describing their particular simulation conditions can be found below:</p> <p>1) DPPC_72_325K (500ns)<br> 2) DPPC_72_310K_rmcomm_leaflets (500ns)<br> 3) DPPC_72_310K_rmcomm_leaflets_low_hydration (500ns)<br> 4) POPC_72_310K (500ns)<br> 5) POPC_72_310K_rmcomm_leaflets (500ns)<br> 6) POPC_72_310K_rmcomm_leaflets_low_hydration (550ns)<br> 7) POPC_72_303K_rmcomm_leaflets_low_hydration (550ns)</p> <p>For further information read the Readme file provided for each simulation.</p>
200 ns simulation of a DMPC bilayer using Gromos 53A6 + Berger lipids
<p><strong>MD simulation of a DMPC bilayer: 200 ns </strong></p> <ul> <li>Gromos 53A6 force field and Berger lipids (lipid.itp)</li> <li>128 DMPC lipids and 3655 SPC waters. Total number of atoms: 16853.</li> <li>This simulation: 200 ns. The systems was equilibrated for 52 ns before this run.</li> <li>Simulation details: <ul> <li>Temperature: 323 K</li> <li>Times step: 2 fs</li> <li>V-rescale thermostat, Parrinello-Rahman barostat, P-LINCS for constraints</li> <li>The run was done using a laptop with GTX980M. Performance: ~105ns/day</li> </ul> </li> <li>Area per lipid and thickness (P-P distance) are provided.</li> </ul>
Molecular dynamics simulation of the permeation of 5ALA across the lipid bilayers of the stratum corneum
<p>Input and output files for US-REST3 MD simulations of the permeation of 5ALA across a lipid bilayer representative of the lipid bilayers of the stratum corneum. Each folder corresponds to US-REST3 and conventional US calculations performer at different distances between the permeant and the centre of mass of the lipid bilayer.</p>
Molecular dynamics simulation of the permeation of Me-5ALA across the lipid bilayers of the stratum corneum
<p>Input and output files for US-REST3 MD simulations of the permeation of Me-5ALA across a lipid bilayer representative of the lipid bilayers of the stratum corneum. Each folder corresponds to US-REST3 and conventional US calculations performer at different distances between the permeant and the centre of mass of the lipid bilayer.</p>
DPPC lipid bilayer simulation with CHARMM36-LJPME force field using OpenMM
<p>DPPC lipid bilayer simulation (300 ns) with CHARMM36-LJPME force field using OpenMM at 323K.</p> <p>Used in <a href="http://doi.org/10.1021/acs.jctc.1c00951">https://doi.org/10.1021/acs.jctc.1c00951</a></p> <p>The force field parameters were downloaded from <a href="https://terpconnect.umd.edu/%7Ejbklauda/ff.html">https://terpconnect.umd.edu/%7Ejbklauda/ff.html</a>.</p> <p><a href="https://zenodo.org/api/files/1e89f677-91a8-472d-aebb-144fddd58d23/trajCORRECT1-2.dcd?versionId=5317fd88-6b98-4905-b171-53c1cd199cfe">trajCORRECT1-2.dcd </a>has incorrect timestamps. traj1-2.xtc has correct timestamps.<br> </p>
Movies of oxidized lipids PoxnoPC and PazePC in POPC bilayers
<p>Movies showing the last 100 ns from 1 microsecond simulations of PoxnoPC-POPC and PazePC-POPC systems. <br> </p> <ul> <li>POPC: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphochol</li> <li>PoxnoPC: 1-palmitoyl-2-(9’-oxo-nonanoyl)-sn-glycero-3-phosphocholin</li> <li>PazePC: 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholin</li> </ul> <p><strong>Reference:</strong></p> <ul> <li><em><strong>Effect of oxidation on POPC lipid bilayers: Anionic carboxyl group plays a major role</strong></em>, Behnaz Bagheri, Phansiri Boonnoy, <a href="https://www.researchgate.net/profile/Jirasak-Wong-Ekkabut">Jirasak Wong-ekkabut</a> and <a href="https://www.researchgate.net/profile/Mikko-Karttunen-2">Mikko Karttunen</a>, PCCP (2023). DOI: <a href="https://doi.org/10.1039/D3CP01692G">https://doi.org/10.1039/D3CP01692G</a> </li> </ul> <p> </p>
Single lipid component membrane bilayer MD with CHARMM36 force field, simulated with the CHARMM program
<p>Data for ten single component lipid bilayer simulations, with 3 files per lipid: a DCD file with coordinates, a PSF file describing the system, and a .zip file containing the starting coordinate set (CHARMM COOR format) and the other inputs used for the CHARMM simulations. Only the POPG system includes ions: Na+ to neutralize the lipids, and ca. 0.15 M NaCl.</p> <p>The DCD trajectory files contain coordinate sets stored at 0.1 ns intervals, <br> and are in the original CHARMM binary format.</p> <p>Lipid Nlpd Nwat ns<br> DLPC 648 25920 200<br> DMPC 648 16632 100<br> DOPC 648 21681 350<br> DOPE 648 21681 350<br> DPPC 648 19701 300<br> POPC 648 20178 200<br> POPE 720 23049 100<br> POPG 648 29160 200<br> PSM 648 18828 200<br> SDPE 648 25920 100</p> <p>"Mechanical properties of lipid bilayers from molecular dynamics simulation",<br> R. M. Venable, F. L. Brown and R. W. Pastor,<br> Chemistry and Physics of Lipids, 192 pp. 60-74 (2015). </p> <p>https://pubmed.ncbi.nlm.nih.gov/26238099/<br> https://www.sciencedirect.com/science/article/pii/S0009308415300190?via%3Dihub</p> <p> See also:</p> <p>"Identifying systematic errors in a power spectral analysis of simulated<br> lipid membranes"<br> Muhammed F. Ergüder, Markus Deserno<br> J. Chem. Phys. 154, 214103 (2021); doi: 10.1063/5.0049448<br> </p> <p> </p>
Data from: Bioinspired design rules for flipping across the lipid bilayer from systematic simulations of membrane protein segments
Open the record for dataset details and reuse information.
Thermal properties of lipid bilayers determined using upconversion nanothermometry
<p>Dataset accompanying figures published in the publication DOI: 10.5281/zenodo.3597416</p>
Slipids-2020 force field for lipid bilayer simulations
<p>Slipids-2020 force field for various lipids<br> -----------------------------------------------------</p> <p>Authors: Joakim Jämbeck, Inna Ermilova, Fredrik Grote, Alexander Lyubartsev<br> Department of Materials and Environmental Chemistry,<br> Stockholm University, Stockholm 10691 Sweden<br> e-mail: alexander.lyubartsev@mmk.su.se<br> 2012 - 2020</p> <p><br> Content:</p> <p>Slipids_2020.ff: directory containing the force field.<br> Included into the Gromacs topology file by: <br> #include "Slipids_2020.ff/forcefield.itp"</p> <p>itp_files: itp files for various lipids<br> boxes: equilibrated configurations for some lipid systems</p> <p>The force field can be used together with the AMBER-family FF for proteins and GAFF for small molecules</p> <p> </p>
Multiscale molecular dynamics simulations of human P-glycoprotein in complex lipid bilayer
<p>The topology (gro) and trajectory (xtc) files for multiscale - coarse-grained (CG) and atomistic (AT) molecular dynamics simulations of human P-glycoprotein in complex lipid bilayer. The coarse grained simulations are 10 microseconds long and the trajectories have 1 frame saved at every 10 ns, while the atomistic simulations are 100 ns long and have 2 frames saved at every nanosecond. </p>
Tracking conformational transitions of the gonadotropin hormone receptors in a bilayer of (SDPC) poly-unsaturated lipids from all-atom molecular dynamics simulations.
<p>In the present study, we describe the results from a computational microscopy perspective (also known as molecular dynamics simulation) at the atomistic resolution for the two gonadotropin hormone receptors, the follicle-stimulant hormone receptor and the luteinizing/chorionic gonadotropin hormone receptor, which are essential for reproduction in humans.</p>
All-atom simulations of DOPE/DOPC lipid bilayers (0%, 50% and 100% DOPC).
<p>All-atom (CHARMM C36) simulations of DOPE/DOPC bilayers (0, 50 and 100 % DOPE). Size sufficient to get the bending modulus and spontaneous curvature difference using our "Spatial Extent" paper methodology.</p><p>DCD format trajectories have frames saved every 0.5 nanoseconds (500 picoseconds).</p><p>Amber dynamics input file included.</p>
Figure Data for "Crystallization of n-alkanes under anisotropic nano-confinement in lipid bilayers"
<p>Data contained in the figures in the preprint entitled "Crystallization of n-alkanes under anisotropic nano-confinement in lipid bilayers"; to be published on ChemRxiv.</p>
Inputs and outputs for bilayers simulations in "Accurate Simulations of Lipid Monolayers Require a Water Model With Correct Surface Tension"
<p>Inputs and outputs file for simulations of POPC and DPPC Bilayers at various temperatures. For details see:</p>
Data for "Electrically Controlling and Optically Observing the Membrane Potential of Supported Lipid Bilayers"
<p>Raw data of all EIS, imaging and time-resolved fluorescence measurements presented in "Electrically Controlling and Optically Observing the Membrane Potential of Supported Lipid Bilayers".</p>
POPG lipid bilayer simulation at T298K ran with MODEL_CHARMM_GUI force field and Gromacs
<p>POPG lipid bilayer simulation at T298K ran 100ns with the force field given by CHARMM gui using Gromacs.</p> <p>118 POPG, 4110 TIP3P and 118 potassium molecules.</p> <p> </p>
Simulations of a POPC lipid bilayer in water solution at various NaCl and CaCl2 concentration with Lipid14, TIP3p and Dang or ECC ions
<p>flat POPC bilayer simulations at various NaCl and CaCl2 concentration</p> <p>modelled with Lipid14 force field, TIP3p water model and Dang or ECC ions.</p> <p>file names report molar fraction of cations (i.e. not bulk concentrations).</p> <p>simulations performed with Gromacs 5.1.4 (*.xtc files) and openMM 7 (*.dcd files)</p> <p>simulation length 300 ns</p> <p>temperature 313 K (otherwise noted)</p>
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